Detecting the outbreak of influenza based on the shortest path of dynamic city network
The influenza pandemic causes a large number of hospitalizations and even deaths. There is an urgent need for an efficient and effective method for detecting the outbreak of influenza so that timely, appropriate interventions can be made to prevent or at least prepare for catastrophic epidemics. In this study, we proposed a computational method, the shortest-path-based dynamical network marker (SP-DNM), to detect the pre-outbreak state of influenza epidemics by monitoring the dynamical change of the shortest path in a city network. Specifically, by mapping the real-time information to a properly constructed city network, our method detects the early-warning signal prior to the influenza outbreak in both Tokyo and Hokkaido for consecutive 9 years, which demonstrate the effectiveness and robustness of the proposed method.
Chen et al. (2020) Detecting the outbreak of influenza based on the shortest path of dynamic city network. PeerJ 8:e9432 https://doi.org/10.7717/peerj.9432
Quantifying local ecological knowledge to model historical abundance of long-lived, heavily-exploited fauna
Deriving robust historical population trends for long-lived species subject to human exploitation is challenging in scenarios where long-term scientific data are scarce or unavailable, as often occurs for species affected by small-scale fisheries and subsistence hunting. The importance of Local Ecological Knowledge (LEK) in data-poor scenarios is increasingly recognized in conservation, both in terms of uncovering historical trends and for engaging community stewardship of historic information. Building on previous work in marine historical ecology and local ecological knowledge, we propose a mixed socio-ecological framework to reliably document and quantify LEK to reconstruct historical population trends. Our method can be adapted by interdisciplinary teams to study various long-lived taxa with a history of human use. We demonstrate the validity of our approach by reconstructing long-term abundance data for the heavily-exploited East Pacific green turtle (Chelonia mydas) in Baja California, Mexico, which was driven to near extinction by a largely unregulated fishery from the early 1950s to the 1980s. No scientific baseline abundance data were available for this time-frame because recent biological surveys started in 1995 after all green turtle fisheries in the area were closed. To fill this data gap, we documented LEK among local fishers using ethnographic methods and obtained verified, qualitative data to understand the socio-environmental complexity of the green turtle fishery. We then established an iterative framework to synthesize and quantify LEK using generalized linear models (GLMs) and nonlinear regression (NLR) to generate a standardized, LEK-derived catch-per-unit-effort (CPUE) time-series. CPUE is an index of abundance that is compatible with contemporary scientific survey data. We confirmed the accuracy of LEK-derived CPUE estimates via comparisons with fisheries statistics available for 1962–1982. We then modeled LEK-derived abundance trends prior to 1995 using NLR. Our model established baseline abundance and described historical declines, revealing that the most critical (exponential) decline occurred between 1960 and 1980. This robust integration of LEK data with ecological science is of critical value for conservation and management, as it contributes to a holistic view of a species’ historic and contemporary conservation status.
Early-Capistrán et al. (2020) Quantifying local ecological knowledge to model historical abundance of long-lived, heavily-exploited fauna. PeerJ 8:e9494 https://doi.org/10.7717/peerj.9494
Engineering of HN3 increases the tumor targeting specificity of exosomes and upgrade the anti-tumor effect of sorafenib on HuH-7 cells
Safe, efficient and cancer cell targeted delivery of CRISPR/Cas9 is important to increase the effectiveness of available cancer treatments. Although cancer derived exosomes offer significant advantages, the fact that it carries cancer related/inducing signaling molecules impedes them from being used as a reliable drug delivery vehicle. In this study, we report that normal epithelial cell-derived exosomes engineered to have HN3 (HN3LC9-293exo), target tumor cells as efficiently as that of the cancer cell-derived exosomes (C9HuH-7exo). HN3LC9-293exo were quickly absorbed by the recipient cancer cell in vitro. Anchoring HN3 to the membrane of the exosomes using LAMP2, made HN3LC9-293exo to specifically enter the GPC3+ HuH-7 cancer cells than the GPC3− LO2 cells in a co-culture model. Further, sgIQ 1.1 plasmids were loaded to exosomes and surprisingly, in combination with sorafenib, synergistic anti-proliferative and apoptotic effect of loaded HN3LC9-293exo was more than the loaded C9HuH-7exo. While cancer-derived exosomes might induce the drug resistance and tumor progression, normal HEK-293 cells-derived exosomes with modifications for precise cancer cell targeting like HN3LC9-293exo can act as better, safe and natural delivery systems to improve the efficacy of the cancer treatments.
He et al. (2020) Engineering of HN3 increases the tumor targeting specificity of exosomes and upgrade the anti-tumor effect of sorafenib on HuH-7 cells. PeerJ 8:e9524 https://doi.org/10.7717/peerj.9524
The importance of open science for biological assessment of aquatic environments
Open science principles that seek to improve science can effectively bridge the gap between researchers and environmental managers. However, widespread adoption has yet to gain traction for the development and application of bioassessment products. At the core of this philosophy is the concept that research should be reproducible and transparent, in addition to having long-term value through effective data preservation and sharing. In this article, we review core open science concepts that have recently been adopted in the ecological sciences and emphasize how adoption can benefit the field of bioassessment for both prescriptive condition assessments and proactive applications that inform environmental management. An example from the state of California demonstrates effective adoption of open science principles through data stewardship, reproducible research, and engagement of stakeholders with multimedia applications. We also discuss technical, sociocultural, and institutional challenges for adopting open science, including practical approaches for overcoming these hurdles in bioassessment applications.
Beck et al. (2020) The importance of open science for biological assessment of aquatic environments. PeerJ 8:e9539 https://doi.org/10.7717/peerj.9539
Application of material from used car tyres in geotechnics—an environmental impact analysis
This work begins with a literature-based discussion of the hazardous-waste problem represented by car tyres as hazardous waste, along with possible ways in which they might be utilised or managed. The impact of the material on the environment is characterised in the process, not least in the context of pollutants leached to the aquatic environment. Input in terms of new research results concerns the impact on water and soil of material from used car tyres being used in geotechnics. Specifically, tyre bales comprising 100–140 car vehicle tyres compressed into a lightweight block and secured by galvanised steel tie wires running around the length and depth of the bale, were researched, having been immersed in basins with alkaline and acidic water following initial preparation and pre-washing. The aim was to in some sense simulate—respectively—conditions in which rain and surface/ground water are involved, or else acid rain. To do that, the tyre bales were placed in the water for 120 days, with emerging leachate analysed after set intervals of time, with a view to changes in key physicochemical parameters of water being noted, as well as signs of the leaching of both undesirable components and priority substances, from tyres into the aqueous medium. Washing of the tyre bales was shown to induce slight pollution of water, with limited exceedance of normative values in respect of OWO content. However, this increase was not due to leaching of the Persistent Organic Pollutants tested for, but may rather have reflected contamination of tyres used, e.g., of soil at the place of previous storage. In general, waste water arising does not therefore contain substances that would stand in the way (legally) of its being discharged into a combined sewer system. Similar conclusions were arrived at through analysis of the leaching of pollutants from tyre bales exposed in the aforementioned pools of water of neutral and acidic reaction. Wastewater arising was not enriched significantly in impurities (be these metals, PAHs, phthalates, selected anions or cations), and there were therefore no exceedances of standards imposed for wastewater discharged to either waters or soil.
Environmental Contamination and Remediation
Duda et al. (2020) Application of material from used car tyres in geotechnics—an environmental impact analysis. PeerJ 8:e9546 https://doi.org/10.7717/peerj.9546
Pots vs trammel nets: a catch comparison study in a Mediterranean small-scale fishery
Passive bottom-set nets are the most widely used fishing gears in Mediterranean small-scale fisheries (SSFs). Trammel nets, in particular, have key advantages such as their ease of use and handling and high capture efficiency for numerous commercial species. However, they entail high discard rates (5–44% of the total catch) connected to high mortality, thus exerting an adverse impact on benthic communities, besides catching individuals of commercial species under the minimum conservation reference size (MCRS) and specimens of protected species. Fish pots are seen as alternative and a more sustainable gear type that allow reducing discards in SSFs. In this study, a collapsible pot was tested at three coastal sites in the north-western Adriatic Sea (GFCM GSA 17) to compare its catch efficiency with that of the local traditional trammel nets. Data analysis demonstrated a similar catch efficiency for the commercial species, both among sites and as a whole. Moreover, the trammel net caught a larger amount of discards, both in terms of species number and of CPUEW. The catch comparison study involved the two most abundant landed species, common cuttlefish Sepia officinalis and annular sea bream Diplodus annularis. The pots were more effective for S. officinalis, whereas the trammel net was more effective for the shorter length classes for D. annularis, which were mostly under the MCRS (12 cm). The innovative pots could provide a valuable alternative to the trammel nets traditionally used in the Adriatic Sea, at least in certain areas and periods. Their main advantages include that they do not require a different rigging and they can be used without bait, while their foldable design allows large numbers to be easily loaded on board SSF vessels. The results of this pilot study indicate that pots can achieve the objectives of reducing discards and bycatch in SSFs without penalizing the catch of commercial species.
Petetta et al. (2020) Pots vs trammel nets: a catch comparison study in a Mediterranean small-scale fishery. PeerJ 8:e9287 https://doi.org/10.7717/peerj.9287
Variation of soil nutrients and bacterial community diversity of different land utilization types in Yangtze River Basin, Chongqing Municipality
The diversity and community distribution of soil bacteria in different land use types in Yangtze River Basin, Chongqing Municipality were studied by using Illumina MiSeq analysis methods. Soil physical and chemical properties were determined, and correlation analyses were performed to identify the key factors affecting bacterial numbers and α-diversity in these soils. The results showed that the soil physical and chemical properties of different land use types decrease in the order: mixed forest (M2) > pure forest (P1) > grassland (G3) > bare land (B4). There were significant differences in bacterial diversity and communities of different land use types. The diversity of different land use types showed the same sequence with the soil physical and chemical properties. The abundance and diversity of bacterial in M2 and P1 soils was significantly higher than that in G3 and B4 soils. At phylum level, G3 and B4 soils were rich in only Proteobacteria and Actinobacteria, whereas M2 and P1 soils were rich in Proteobacteria, Actinobacteria and Firmicutes. At genus level, Faecalibacterium and Agathobacter were the most abundant populations in M2 soil and were not found in other soils. Pearson correlation analysis showed that soil moisture content, pH, AN, AP, AK and soil enzyme activity were significantly related to bacterial numbers, diversity and community distribution.
Li et al. (2020) Variation of soil nutrients and bacterial community diversity of different land utilization types in Yangtze River Basin, Chongqing Municipality. PeerJ 8:e9386 https://doi.org/10.7717/peerj.9386
Biodiversity of carapace epibiont diatoms in loggerhead sea turtles (Caretta caretta Linnaeus 1758) in the Aegean Sea Turkish coast
Background The Aegean Sea coast of Turkey hosts one of the most important nesting grounds for loggerhead sea turtles (Caretta caretta) in the Mediterranean Sea. Previous studies have revealed that the sea turtle carapace provides favourable conditions for various epibiontic organisms. Epibionts occurring on the carapace have been examined from different locations in the oceans. Methods This is the first time such a high number (39) of samples collected from nesting turtles during such a long time period (extending from 2011 to 2018) has been used for the study of the diatom component of the microbiome on the turtle carapaces. A total of 33 samples were investigated in terms of light microscopy (LM) and scanning electron microscopy (SEM). Six unprocessed biofilm fragments were subject to SEM observations. Results A total of 457 epizoic diatom taxa belonging to 86 genera were identified. Epizoic forms, e.g., Achnanthes spp., Chelonicola spp. or Tripterion spp. (also identified by SEM observations of the undisturbed pieces of the microbiome) dominated in terms of relative abundance, but the highest numbers of taxa were ubiquitously represented by Navicula (79), Nitzschia (45), Amphora (40), Cocconeis (32), Diploneis (25) and Mastogloia (23). Navicula perminuta and Delphineis australis were the most frequent taxa, present in 65% of the samples, both with an average relative abundance of 10%. The results of our study revealed that diatoms are an essential component of the loggerhead sea turtles’ microbiome, in terms of high biodiversity and abundance. Although strict epibionts provide a signature of the turtle microbiome, the carapace as a solid substrate attracts numerous benthic diatom species which are considered opportunistic forms and can be found in the surrounding benthic habitats of the vast ocean littoral space.
Kaleli et al. (2020) Biodiversity of carapace epibiont diatoms in loggerhead sea turtles (Caretta caretta Linnaeus 1758) in the Aegean Sea Turkish coast. PeerJ 8:e9406 https://doi.org/10.7717/peerj.9406
An updated genetic marker for detection of Lake Sinai Virus and metagenetic applications
Background Lake Sinai Viruses (LSV) are common RNA viruses of honey bees (Apis mellifera) that frequently reach high abundance but are not linked to overt disease. LSVs are genetically heterogeneous and collectively widespread, but despite frequent detection in surveys, the ecological and geographic factors structuring their distribution in A. mellifera are not understood. Even less is known about their distribution in other species. Better understanding of LSV prevalence and ecology have been hampered by high sequence diversity within the LSV clade. Methods Here we report a new polymerase chain reaction (PCR) assay that is compatible with currently known lineages with minimal primer degeneracy, producing an expected 365 bp amplicon suitable for end-point PCR and metagenetic sequencing. Using the Illumina MiSeq platform, we performed pilot metagenetic assessments of three sample sets, each representing a distinct variable that might structure LSV diversity (geography, tissue, and species). Results The first sample set in our pilot assessment compared cDNA pools from managed A. mellifera hives in California (n = 8) and Maryland (n = 6) that had previously been evaluated for LSV2, confirming that the primers co-amplify divergent lineages in real-world samples. The second sample set included cDNA pools derived from different tissues (thorax vs. abdomen, n = 24 paired samples), collected from managed A. mellifera hives in North Dakota. End-point detection of LSV frequently differed between the two tissue types; LSV metagenetic composition was similar in one pair of sequenced samples but divergent in a second pair. Overall, LSV1 and intermediate lineages were common in these samples whereas variants clustering with LSV2 were rare. The third sample set included cDNA from individual pollinator specimens collected from diverse landscapes in the vicinity of Lincoln, Nebraska. We detected LSV in the bee Halictus ligatus (four of 63 specimens tested, 6.3%) at a similar rate as A. mellifera (nine of 115 specimens, 7.8%), but only one H. ligatus sequencing library yielded sufficient data for compositional analysis. Sequenced samples often contained multiple divergent LSV lineages, including individual specimens. While these studies were exploratory rather than statistically powerful tests of hypotheses, they illustrate the utility of high-throughput sequencing for understanding LSV transmission within and among species.
Iwanowicz et al. (2020) An updated genetic marker for detection of Lake Sinai Virus and metagenetic applications. PeerJ 8:e9424 https://doi.org/10.7717/peerj.9424
Mesozooplankton grazing minimally impacts phytoplankton abundance during spring in the western North Atlantic
The impacts of grazing by meso- and microzooplankton on phytoplankton primary production (PP) was investigated in the surface layer of the western North Atlantic during spring. Shipboard experiments were performed on a latitudinal transect at three stations that differed in mixed layer depth, temperature, and mesozooplankton taxonomic composition. The mesozooplankton community was numerically dominated by Calanus finmarchicus at the northern and central station, with Calanus hyperboreus also present at the northern station. The southern station was >10 °C warmer than the other stations and had the most diverse mesozooplankton assemblage, dominated by small copepods including Paracalanus spp. Microzooplankton grazing was detected only at the northern station, where it removed 97% of PP. Estimated clearance rates by C. hyperboreus and C. finmarchicus suggested that at in-situ abundance these mesozooplankton were not likely to have a major impact on phytoplankton abundance, unless locally aggregated. Although mesozooplankton grazing impact on total phytoplankton was minimal, these grazers completely removed the numerically scarce > 10 µm particles, altering the particle-size spectrum. At the southern station, grazing by the whole mesozooplankton assemblage resulted in a removal of 14% of PP, and its effect on net phytoplankton growth rate was similar irrespective of ambient light. In contrast, reduction in light availability had an approximately 3-fold greater impact on net phytoplankton growth rate than mesozooplankton grazing pressure. The low mesozooplankton grazing impact across stations suggests limited mesozooplankton-mediated vertical export of phytoplankton production. The constraints provided here on trophic transfer, as well as quantitative estimates of the relative contribution of light and grazer controls of PP and of grazer-induced shifts in particle size spectra, illuminate food web dynamics and aid in parameterizing modeling-frameworks assessing global elemental fluxes and carbon export.
Morison et al. (2020) Mesozooplankton grazing minimally impacts phytoplankton abundance during spring in the western North Atlantic. PeerJ 8:e9430 https://doi.org/10.7717/peerj.9430